Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus

IMPORTANCE

Staphylococcus saprophyticus is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of S. saprophyticus recovered from urine specimens. However, TMP-SMX-resistant S. saprophyticus has been detected recently in UTI patients, as well as in our cohort. Herein, we investigated the understudied resistance patterns of this pathogenic species by linking genomic antibiotic resistance gene (ARG) content to susceptibility phenotypes. We describe ARG associations with known and novel SCCmec configurations as well as phage elements in S. saprophyticus, which may serve as intervention or diagnostic targets to limit resistance transmission. Our analyses yielded a comprehensive database of phenotypic data associated with the ARG sequence in clinical S. saprophyticus isolates, which will be crucial for resistance surveillance and prediction to enable precise diagnosis and effective treatment of S. saprophyticus UTIs.

A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC

The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.

Use of genome sequencing to resolve differences in gradient diffusion and agar dilution antimicrobial susceptibility testing performance of Neisseria gonorrhoeae isolates in Alberta, Canada

Agar dilution is the gold standard method for phenotypic antimicrobial susceptibility testing (AST) for Neisseria gonorrhoeae. However, this method is laborious and requires expertise, so laboratories that perform N. gonorrhoeae AST may choose alternative methods such as disk diffusion and gradient diffusion. In this study, we retrospectively compare the performance of gradient diffusion to agar dilution for 2,394 unique N. gonorrhoeae isolates identified in Alberta from 2017 to 2020 against azithromycin, cefixime, ceftriaxone, ciprofloxacin, penicillin, and tetracycline. Genome sequencing was utilized to resolve discrepancies between AST methods, detect antimicrobial resistance markers, and identify trends between error rates and sequence types (STs) of isolates. Over 90% of N. gonorrhoeae isolates were susceptible to azithromycin, cefixime, and ceftriaxone, whereas decreased susceptibility was observed for ciprofloxacin, penicillin, and tetracycline. Categorical (CA) and essential agreement (EA) was poorest between the two methods for penicillin (CA: 86.02%; EA: 77.69%) and tetracycline (CA: 47.22%; EA: 55.96%); however, the low CA was primarily attributed to minor errors. Antimicrobial agents with errors outside of acceptable limits included azithromycin (very major error: 18.42%; major error: 7.73%) and tetracycline (very major error: 6.17%). Genome sequencing on a subset of isolates resolved 30.3% of the azithromycin major errors and confirmed the azithromycin or tetracycline very major errors. Significant associations between certain STs and error types for azithromycin and tetracycline were also identified. Overall, gradient diffusion compared well to agar dilution for cefixime, ceftriaxone, and ciprofloxacin, and genome sequencing was identified as a useful tool to arbitrate discrepant susceptibility testing results between gradient diffusion and agar dilution for N. gonorrhoeae.

Three separate acquisitions of blaNDM-1 in three different bacterial species from a single patient

To investigate the acquisition and relatedness of New Delhi Metallo-beta-lactamase among multiple separate species from one patient. Five isolates from three species (Pseudomonas aeruginosa; Pa, Acinetobacter baumannii; Ab and Proteus mirabilis; Pm) suspected of harbouring a carbapenemase were investigated by phenotype (antimicrobial susceptibilities) and whole genome sequencing. Epidemiological data was collected on this patient. Three different carbapenemase genes were detected; blaVIM-1 (Pa; ST773), blaOXA-23 (Ab, ST499) and blaNDM-1 identified in all isolates. NDM regions were found chromosomally integrated in all isolates. Data showed no evidence of NDM-1 transfer within this patient suggesting the enzyme was acquired in three separate events.

Antimicrobial stewardship, procalcitonin testing, and rapid blood-culture identification to optimize sepsis care in critically ill adult patients: A quality improvement initiative

We examined the effect of an antimicrobial stewardship program (ASP), procalcitonin testing and rapid blood-culture identification on hospital mortality in a prospective quality improvement project in critically ill septic adults. Secondarily, we have reported antimicrobial guideline concordance, acceptance of ASP interventions, and antimicrobial and health-resource utilization.

A two-ward acute care hospital outbreak of SARS-CoV-2 delta variant including a point-source outbreak associated with the use of a mobile vital signs cart and sub-optimal doffing of personal protective equipment

BACKGROUND

The arrival of the Delta variant of SARS-CoV-2 was associated with increased transmissibility and illness of greater severity. Reports of nosocomial outbreaks of Delta variant COVID-19 in acute care hospitals have been described but control measures varied widely.

AIM

Epidemiological investigation of a linked two-ward COVID-19 Delta variant outbreak was conducted to elucidate its source, risk factors, and control measures.

METHODS

Investigations included epidemiologic analysis, detailed case review serial SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) testing of patients and healthcare workers (HCWs), viral culture, environmental swabbing, HCW-unaware personal protective equipment (PPE) audits, ventilation assessments, and the use of whole genome sequencing (WGS).

FINDINGS

This linked two-ward outbreak resulted in 17 patient and 12 HCW cases, despite an 83% vaccination rate. In this setting, suboptimal adherence and compliance to PPE protocols, suboptimal hand hygiene, multi-bedded rooms, and a contaminated vital signs cart with potential fomite or spread via the hands of HCWs were identified as significant risk factors for nosocomial COVID-19 infection. Sudden onset of symptoms, within 72 h, was observed in 79% of all Ward 2 patients, and 93% of all cases (patients and HCWs) on Ward 2 occurred within one incubation period, consistent with a point-source outbreak. RT-PCR assays showed low cycle threshold (C_T) values, indicating high viral load from environmental swabs including the vital signs cart. WGS results with ≤3 SNP differences between specimens were observed.

CONCLUSION

Outbreaks on both wards settled rapidly, within 3 weeks, using a `back-to-basics' approach without extraordinary measures or changes to standard PPE requirements. Strict adherence to recommended PPE, hand hygiene, education, co-operation from HCWs, including testing and interviews, and additional measures such as limiting movement of patients and staff temporarily were all deemed to have contributed to prompt resolution of the outbreak.

Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019-June 2021)

Background

Pneumonia from SARS-CoV-2 is difficult to distinguish from other viral and bacterial etiologies. Broad-spectrum antimicrobials are frequently prescribed to patients hospitalized with COVID-19 which potentially acts as a catalyst for the development of antimicrobial resistance (AMR).

Objectives

We conducted a systematic review and meta-analysis during the first 18 months of the pandemic to quantify the prevalence and types of resistant co-infecting organisms in patients with COVID-19 and explore differences across hospital and geographic settings.

Methods

We searched MEDLINE, Embase, Web of Science (BioSIS), and Scopus from November 1, 2019 to May 28, 2021 to identify relevant articles pertaining to resistant co-infections in patients with laboratory confirmed SARS-CoV-2. Patient- and study-level analyses were conducted. We calculated pooled prevalence estimates of co-infection with resistant bacterial or fungal organisms using random effects models. Stratified meta-analysis by hospital and geographic setting was also performed to elucidate any differences.

Results

Of 1331 articles identified, 38 met inclusion criteria. A total of 1959 unique isolates were identified with 29% (569) resistant organisms identified. Co-infection with resistant bacterial or fungal organisms ranged from 0.2 to 100% among included studies. Pooled prevalence of co-infection with resistant bacterial and fungal organisms was 24% (95% CI 8–40%; n = 25 studies: I² = 99%) and 0.3% (95% CI 0.1–0.6%; n = 8 studies: I² = 78%), respectively. Among multi-drug resistant organisms, methicillin-resistant Staphylococcus aureus, carbapenem-resistant Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and multi-drug resistant Candida auris were most commonly reported. Stratified analyses found higher proportions of AMR outside of Europe and in ICU settings, though these results were not statistically significant. Patient-level analysis demonstrated > 50% (n = 58) mortality, whereby all but 6 patients were infected with a resistant organism.

Conclusions

During the first 18 months of the pandemic, AMR prevalence was high in COVID-19 patients and varied by hospital and geography although there was substantial heterogeneity. Given the variation in patient populations within these studies, clinical settings, practice patterns, and definitions of AMR, further research is warranted to quantify AMR in COVID-19 patients to improve surveillance programs, infection prevention and control practices and antimicrobial stewardship programs globally.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-022-01085-z.

Association between Gut Colonization of Vancomycin-resistant Enterococci and Liver Transplant Outcomes

BACKGROUND

Vancomycin-resistant enterococci (VRE) colonization is common in liver transplant recipients and has been associated with worse post-transplant outcomes.

METHODS

We conducted a retrospective cohort study at the University of Alberta Hospital including patients who underwent a liver transplant between September 2014 and December 2017.

RESULTS

Of 343 patients, 68 (19.8%) had pre-transplant VRE colonization and 27 (27/275, 9.8%) acquired VRE post-transplant, 67% were males and the median age was 56.5 years. VRE colonized patients at baseline had higher MELD scores and required longer post-transplant hospitalization. VRE colonization was associated with increased risk of early acute kidney injury (AKI) (64% vs 52%, p = 0. 044), clinically significant bacterial/fungal infection (29% vs 17%, p = 0. 012) and invasive VRE infection (5% vs 1%, p = 0. 017). Mortality at 2-years was 13% in VRE-colonized versus 7% in non-colonized (p = 0.085). On multivariate analysis, VRE colonization increased the risk of post-transplant AKI (HR 1.504, 95% CI: 1.077-2.100, p = 0.017) and clinically significant bacterial or fungal infection at 6 months (HR 2.038, 95%CI: 1.222-3.399, p = 0.006), and was associated with non-significant trend towards increased risk of mortality at 2-years post-transplant (HR 1.974 95% CI 0.890-4.378; p = 0.094).

CONCLUSIONS

VRE colonization in liver transplant patients is associated with increased risk of early AKI, clinically significant infections, and a trend towards increased mortality at 2-years. This article is protected by copyright. All rights reserved.

Four genomic clades of Candida auris identified in Canada, 2012-2019

Candida auris is an emerging yeast that is associated with antifungal resistance and healthcare-associated outbreaks. From 2012-2019, there were 24 known cases of C. auris colonization or infection in Canada. Isolates were from axilla/groin (n = 6), ear (n = 5), blood (n = 4), toe (n = 2), and a variety of other sites (n = 7). Canadian isolates belonged to the four main genomic clades: Clade I (formerly called South Asian clade, n = 12), Clade II (East Asian, n = 3), Clade III (African, n = 4), and Clade IV (South American, n = 5).  Isolates within each clade were clonal, however, whole genome sequencing may be helpful in identifying clusters within healthcare facilities.

184. Staphylococcus aureus Bacteremia Management and Outcomes Following Infectious Disease Consult Over Time at a Tertiary Care Center in Canada

Background

Staphylococcus aureus bacteremia (SAB) is associated with high morbidity and mortality. Infectious disease consultation (IDC) is associated with increased adherence to guideline management and improved patient outcomes. We describe the IDC rate over time and impact of IDC on the management and outcomes of patients with SAB.

Methods

This retrospective chart review includes adult patients (≥ 18 years) hospitalized at the University of Alberta Hospital, Edmonton, Canada who had at least 1 blood culture growing Staphylococcus aureus during two time periods (A: Jan 2010 to Dec 2012; B: Jan to Oct 2020). Patients who died or were made palliative within 48hrs following bacteremia were excluded. Descriptive statistics were used to compare appropriateness of SAB management and outcomes in patients receiving IDC and those who did not (NIDC).

Results

325 patients in period A and 129 in period B were included. Baseline demographics were similar. IDC rate increased from 63% to 88% (p< 0.001) between the study periods. IDC was associated with increased odds of receiving an echocardiogram (OR=3.56, 95% CI 2.22 – 5.57; OR=20.4, 95% 4.13 – 110.6, p< 0.001) and appropriate duration of antimicrobial therapy (OR=6.74, 95% 3.93 – 11.54; OR=43.2, 95% 5.72 – 529.5, p< 0.001) between study periods. Mean length of stay decreased in patients receiving IDC (44.8 vs 28.1 days, p=0.005) and increased in NIDC patients (19.9 vs 28.7 days, p=0.216). IDC was associated with lower 30-day mortality in period A (OR=3.53, 95% 1.95 – 6.36), however this association was not observed in period B (OR=1.43, 95% 0.40 – 5.56). There was a trend towards decreased odds of mortality in patients receiving early IDC (≤2 days from bacteremia, n=65) compared to late IDC (≥3 days from bacteremia, n=45) (OR=2.59, 95% 0.95 – 7.10, p=0.077).

Conclusion

Our centre’s IDC rate for SAB increased over time without specific intervention. IDC increased the odds of appropriate SAB management and was associated with decreased length of stay in period B. IDC was associated with lower 30-day mortality in period A and trended towards lower mortality in period B. Specifically, early IDC decreased odds of 30-day mortality compared to late IDC. These results suggest that routine early IDC be part of SAB management.

Disclosures

All Authors: No reported disclosures

10. Impact of Infectious Disease Consultation and Theoretical Management Bundle in Patients with Candidemia

Background

Candidemia is associated with significant morbidity and mortality. The impact of infectious diseases consultation (IDC) on clinical outcomes in patients with candidemia is not well established. We evaluated the impact of IDC and a management bundle on clinical outcomes in patients with candidemia.

Methods

A retrospective chart review of adult (age ≥ 18 years) patients with at least 1 blood culture growing Candida species identified at Alberta Precision Laboratories between December 1, 2019 to November 30, 2020 and hospitalized at the University of Alberta Hospital, Edmonton, Canada were included. Patients who died within 48 hours and those who left against medical advice within 24 hours of initial positive blood culture result were excluded. Demographics, management, and outcome data were collected. A complete management bundle was defined as having all the following elements performed: IDC, repeat blood cultures, empiric echinocandin therapy, ophthalmology consult, and echocardiogram.

Results

Thirty-one patients were included for study; mean age was 56 ± 17 years and 65% were male. 14 (45%) cases were admitted under critical care, 7 (23%) surgery, and 10 (32%) medicine. 3/17 (18%) required intensive care unit admission following candidemia diagnosis. Candida albicans was identified in more than half the cases. The primary source was intra-abdominal in 12 (39%), central-line associated in 8 (26%), and urinary in 6 (19%). IDC occurred in 27 cases (87%), echocardiogram in 22 (71%), ophthalmology consult in 10 (32%), and follow-up blood cultures in 30 (97%). 20 (65%) patients received empiric echinocandin. Of the remainder who received empiric fluconazole, 4 (36%) grew non albicans Candida species.

Higher in-hospital mortality was observed in cases without IDC than those with IDC (4/4, 100% vs 8/27, 29.6%, p=0.016) and in those that did not have a complete bundle (12/25, 48% vs 0/6, p=0.059). However, IDC was not associated with the receipt of individual bundle components nor the complete bundle (p=NS).

Conclusion

In patients with candidemia, lower in-hospital mortality was observed in patients who received IDC. Larger studies are required to confirm our findings and assess whether the implementation of a candidemia management bundle is beneficial.

Disclosures

Dima Kabbani, MD, AVIR Pharma (Grant/Research Support, Other Financial or Material Support, Speaker)Edesa Biotech (Scientific Research Study Investigator)Merck (Scientific Research Study Investigator)

Species distribution and antifungal susceptibility of invasive Candida isolates from Canadian hospitals: results of the CANWARD 2011-16 study

OBJECTIVES

Understanding the epidemiology of invasive Candida infections is essential to patient management decisions and antifungal stewardship practices. This study characterized the species distribution and antifungal susceptibilities of prospectively collected isolates of Candida species causing bloodstream infections (BSIs) in patients admitted to tertiary care hospitals located in 14 cities across 8 of the 10 Canadian provinces between 2011 and 2016.

METHODS

Antifungal susceptibility testing was performed by broth microdilution using CLSI methods, breakpoints and epidemiological cut-off values. DNA sequencing of fks loci was performed on all echinocandin-non-susceptible isolates.

RESULTS

Candida albicans (49.6%), Candida glabrata (20.8%) and Candida parapsilosis complex (12.0%) were the most common species out of 1882 isolates associated with BSIs. Candida tropicalis (5.2%), Candida krusei (4.3%), Candida dubliniensis (4.1%), Candida lusitaniae (1.4%) and Candida guilliermondii (1.1%) were less frequently isolated. Between 2011 and 2016, the proportion of C. albicans significantly decreased from 60.9% to 42.1% (P < 0.0001) while that of C. glabrata significantly increased from 16.4% to 22.4% (P = 0.023). C. albicans (n = 934), C. glabrata (n = 392) and C. parapsilosis complex (n = 225) exhibited 0.6%, 1.0% and 4.9% resistance to fluconazole and 0.1%, 2.5% and 0% resistance to micafungin, respectively. Mutations in fks hot-spot regions were confirmed in all nine micafungin non-susceptible C. glabrata.

CONCLUSIONS

Antifungal resistance in contemporary isolates of Candida causing BSIs in Canada is uncommon. However, the proportion of C. glabrata isolates has increased and echinocandin resistance in this species has emerged. Ongoing surveillance of local hospital epidemiology and appropriate antifungal stewardship practices are necessary to preserve the utility of available antifungal agents.

High Rates of Influenza-Associated Invasive Pulmonary Aspergillosis May Not Be Universal: A Retrospective Cohort Study from Alberta, Canada

From 2014–2019, invasive pulmonary aspergillosis complicated 7.2% (0–23.1% in different influenza seasons) of cases of influenza-associated respiratory failure in Edmonton, Alberta. Disease outcomes ranged from survival without therapy to death despite antifungals. Clinician vigilance, longitudinal local surveillance, and refined criteria to identify patients requiring therapy are needed.

The impact of blood culture identification by MALDI-TOF MS on the antimicrobial management of pediatric patients

OBJECTIVE

To assess the impact of MALDI-TOF MS coupled with antimicrobial stewardship on clinical outcomes for pediatric inpatients with bloodstream infections.

METHODS

Outcomes of pediatric inpatients were compared before and after MALDI-TOF MS implementation. Outcomes measured included time until organism identification and susceptibility, duration of antibiotics, patient length of stay (LOS), mortality and hospital costs.

RESULTS

210 and 135 patient events were compared pre- and post-intervention. Average time to organism identification decreased from 41 to 11 hours (P = <0.0001). Time to i) susceptibilities decreased from 50.8 to 37.7 hours (P = <0.0001), ii) de-escalation of antibiotics decreased from 58 to 23 hours (P = <0.0001), iii) discontinuation of unnecessary antibiotics decreased from 49 to 20 hours (P = <0.0001). Infection-related LOS decreased from 10.5 to 8.37 days (P = 0.006). No significant differences were seen for other outcomes.

CONCLUSIONS

MALDI-TOF MS identification of bacteria from blood culture broth improves time to appropriate antibiotic treatment for pediatric inpatients.

Retrospective report of antimicrobial susceptibility observed in bacterial pathogens isolated from ocular samples at Mount Sinai Hospital, 2010 to 2015

BACKGROUND

Antimicrobial resistance has emerged as a major threat to global public health. Thus, the surveillance of changes in antimicrobial resistance in local and global settings is a paramount necessity. While many studies have tracked antimicrobial resistance, only a small percentage surveyed ocular isolates. The purpose of this study was to report the in vitro susceptibility of bacterial pathogens isolated from ocular samples in New York, NY from 2010 to 2015.

METHODS

A retrospective review of ocular isolates was conducted. All organisms were collected by 25 separate inpatient wards and outpatient clinics, and were analyzed by the clinical microbiology laboratory at Mount Sinai Hospital. Clinical Laboratory and Standards Institute (CLSI) guidelines were followed for susceptibility testing and breakpoint interpretations.

RESULTS

A total of 549 bacterial organisms were isolated from 1664 cultures (33%) during the 6-year study period. Of these, 358 isolates (65.2%) underwent susceptibility testing. 182 (50.8%) isolates were Gram-positive. The most common Gram-positive bacterium was Staphylococcus aureus (62.1%). Methicillin-resistance decreased in S. aureus isolates (31.3% in 2010, 14.1% in 2015) but was without significant change (p = 0.25). When analyzing all S. aureus isolates recovered during the study period, there were significantly more methicillin-resistant S. aureus (MRSA) isolates resistant to fluoroquinolones (p <0.0001), erythromycin (p <0.0001), and trimethoprim/sulfamethoxazole (TMP/SMZ; p <0.05). Overall, Streptococcus pneumoniae isolates showed reduced susceptibility to erythromycin, but were otherwise susceptible to the other antimicrobials tested. Haemophilus influenzae (26.1%) and Pseudomonas aeruginosa (23.9%) were the most common Gram-negative bacteria isolated. Resistance to ampicillin and TMP/SMZ was observed in several of the H. influenzae isolates. P. aeruginosa isolates did not show high resistance overall, however, it was noted that isolates resistant to meropenem were also resistant to other antimicrobials (p < 0.01).

CONCLUSION

Overall, antimicrobial resistance was infrequent for the Gram-negative and Gram-positive bacteria analyzed. While the MRSA isolates demonstrated increased resistance to multiple antimicrobial classes, this is expected for this pathogen. Due to the continued use of broad-spectrum oral and systemic antimicrobials to treat ocular infections, findings of this study and other surveillance studies specific to ocular isolates should be used as resources in effective decision making in the treatment of ocular disease.

Report of two paediatric cases of central line infections caused by species of the genus Kocuria

Introduction:

Species of the genus Kocuria are Gram-positive cocci of the family Micrococcacceae that are ubiquitous in the environment and part of the normal skin and oral flora in humans. A paucity of cases have been reported of Kocuria as human pathogens and there are currently no evidence-based guidelines for managing these uncommon infections.

Case presentation:

We present two paediatric cases of central line infections with species of the genus Kocuria that required line removal despite antimicrobial therapy.

Conclusion:

Species of the genus Kocuria are uncommon human pathogens that have rarely been reported to cause opportunistic infections in both adult and paediatric populations. The cases presented here add to the growing body of literature documenting the pathogenicity of these organisms and the possible need for line removal to achieve clinical cure in central line-associated bacteraemia caused by species of the genus Kocuria.

Reflexive culture in adolescents and adults with group A streptococcal pharyngitis

BACKGROUND

Guidelines currently provide conflicting recommendations regarding the diagnosis of group A streptococcal (GAS) pharyngitis in adults. Clinical guidelines state that negative rapid antigen detection tests (RADTs) do not require confirmation by a backup method in adults, whereas laboratory-based guidelines mandate confirmation of a negative RADT in patients of all ages. The objective of this study was to assess the utility of reflexive culture following a negative RADT in adolescents and adults with suspected GAS pharyngitis.

METHODS

A retrospective analysis of 726 patients, aged ≥13 years, with negative RADTs and positive GAS throat cultures, was performed between 1 January 2000 and 31 December 2011 at 2 academic medical centers in Seattle, Washington. Complication rates, treatment, modified Centor score, and bacterial burden in patients with negative RADTs and positive GAS throat cultures were assessed.

RESULTS

Modified Centor scores ≥2 were observed in 55% of patients with a negative RADT and positive GAS culture. Of these, 77% of patients had a moderate or heavy bacterial burden (≥2+). RADTs failed to detect some patients who presented with serious complications of GAS pharyngitis: 29 (4.0%) had peritonsillar abscesses and 2 (0.28%) were diagnosed with acute rheumatic fever. Providers found culture results to be useful for initiating antibiotic therapy or confirming a clinical diagnosis. Antibiotic treatment was prescribed in 68.7% of patients, with culture-directed initiation of therapy documented in 43.5%.

CONCLUSIONS

Reflexive GAS culture is clinically useful when RADTs are negative. RADTs fail to detect a substantial number of adult patients with clinically significant pharyngitis who can benefit from treatment.

Maldi-tof mass spectrometry for microorganism identification

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, reliable, and high-throughput diagnostic tool for the identification of microorganisms. The technology is unique in clinical microbiology, allowing laboratories to definitively identify bacterial and fungal isolates within minutes. The rapid turnaround time and minimal cost for consumables per specimen compared with conventional identification methods have resulted in MALDI-TOF MS being increasingly used in clinical laboratories worldwide. This article summarizes the current literature on MALDI-TOF MS for microbial identification and provides a preview of the method's potential future applications in clinical microbiology.

Binding of Clostridium difficile toxins to human milk oligosaccharides

The binding of recombinant fragments of the C-terminal cell-binding domains of the two large exotoxins, toxin A (TcdA) and toxin B (TcdB), expressed by Clostridium difficile and a library consisting of the most abundant neutral and acidic human milk oligosaccharides (HMOs) was examined quantitatively at 25°C and pH 7 using the direct electrospray ionization mass spectrometry (ES-MS) assay. The results of the ES-MS measurements indicate that both toxin fragments investigated, TcdB-B1 and TcdA-A2, which possess one and two carbohydrate binding sites, respectively, bind specifically to HMOs ranging in size from tri- to heptasaccharides. Notably, five of the HMOs tested bind to both toxins: Fuc(α1-2)Gal(β1-4)Glc, Gal(β1-3)GlcNAc(β1-3)Gal(β1-4)Glc, Fuc(α1-2)Gal(β1-3)GlcNAc(β1-3)Gal(β1-4)Glc, Gal(β1-3)[Fuc(α1-4)]GlcNAc(β1-3)Gal(β1-4)Glc and Gal(β1-4)[Fuc(α1-3)]GlcNAc(β1-3)Gal(β1-4)Glc. However, the binding of the HMOs is uniformly weak, with apparent affinities ≤10(3 )M(-1). The results of molecular docking simulations, taken together with the experimental binding data, suggest that a disaccharide moiety (lactose or lactosamine) represents the core HMO recognition element for both toxin fragments. The results of a Verocytotoxicity neutralization assay reveal that HMOs do not significantly inhibit the cytotoxic effects of TcdA or TcdB. The absence of protection is attributed to the very weak intrinsic affinities that the toxins exhibit towards the HMOs.